Dog genome sequence completed

A female boxer dog has provided the DNA for the first complete sequence of the dog genome, putting into the doghouse the patchy, 80% coverage of a poodle called Shadow, published two years ago.

A publicly funded consortium led by Kerstin Lindblad-Toh of the Broad Institute, in Cambridge, Massachusetts, US, used the shotgun sequencing technique to map the genome of Tasha, an inbred boxer. With this technique the genome is first broken into fragments and the DNA sequence of each determined. Then a computer stitches the fragments back together.

The process must be repeated several times to ensure accuracy, and the new draft is the product of 7.5 repetitions. The genome of Shadow, the poodle owned by gene-entrepreneur Craig Venter, had only 1.5 times coverage. The boxer was chosen as it is highly inbred. That means the difference between its paired chromosomes are smaller, making sequencing easier.

Domestic dogs vary wildly in appearance, yet their genomes are 99.85% similar. The boxer and the poodle, for example, differ by about a single nucleotide change in every 900 bases. “A dog is a dog in a genomic sense,” says Lindblad-Toh.

That is very cool!!
I bet we shall now learn a lot about our own DNA by comparing to the same sequence in dogs. A direct application (as also mentioned) would be for genetic diseases that dogs and humans have in common.

They show how closely related a boxer and a poodle are by saying there is only a single nucleotide change in every 900 bases. But later they say they've catalogued some 2.5 million individual DNA differences between breeds.. For 2.5 million differences to be a small number, I wonder how large is the number of base pairs they have in common??

I remember when they first sequenced the human genome and couldn't figure out what the non-coding sequences were useful for.. In this article they say, much of the non-coding DNA in dogs, is the same as that in humans. That suggests these sequences must serve some function. If dogs and humans share a common ancestor, some of these non-coding sequences would make it through to both animals today. Geneticists should know how many base pair differences ought to be expected since the time the split in our family tree occured, and compare that figure to the number we actually have between the two sequenced genomes.

Here is a comment they made that does not make sense to me:
"Dogs also have more genes in common with humans than do mice, despite splitting from our common ancestor before mice did." How could that be? Unless we got it wrong and mice actually split off the tree before dogs did.